The sea lamprey, Petromyzon marinus, is an emerging nonmammalian model organism that satisfactorily meets the criteria for PA-07-457. The genome has been sequenced to 9.1X coverage and an assembly is publicly available. The impetus for this proposal is based on our observations concerning the dynamic nature of the sea lamprey genome. We have recently shown that P. marinus undergoes substantial chromatin diminution with as much as 20% of its somatic genome being discarded during early embryogenesis. Extensive preliminary data presented in this proposal confirm these losses and importantly corroborate our prior observations that large swaths of protein-coding sequences are also being developmentally eliminated. These findings uncover a severe deficiency in the available lamprey genome sequence assembly. In this application we propose to generate and assemble DNA sequences from the P. marinus germline that will provide an overall improved genome assembly for this species. The proposed work fills a major gap in sequence knowledge for this organism and is therefore critical to nearly every lab that utilizes lamprey as a primary model or as a reference for understanding basal features of vertebrate development, physiology, or genome biology. By developing seeded assemblies of unsampled regions, improving contiguity of the somatic and germline genome assemblies, cross-informing existing clone resources, and annotating the location of expressed sequences within constant and modified regions of the genome, we stand to dramatically improve the utility of existing lamprey genome resources for the community and to learn much about programmed genome rearrangement in this nonmammalian model system.